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- PDB-3ewz: human orotidyl-5'-monophosphate decarboxylase in complex with 5-c... -

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Basic information

Entry
Database: PDB / ID: 3ewz
Titlehuman orotidyl-5'-monophosphate decarboxylase in complex with 5-cyano-UMP
ComponentsOrotidine-5'-phosphate decarboxylase
KeywordsLYASE / decarboxylase / tim barrel / unusual catalysis / Alternative splicing / Disease mutation / Glycosyltransferase / Multifunctional enzyme / Polymorphism / Pyrimidine biosynthesis / Transferase
Function / homology
Function and homology information


UMP biosynthetic process / orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / pyrimidine nucleobase biosynthetic process / Pyrimidine biosynthesis / orotidine-5'-phosphate decarboxylase / UDP biosynthetic process / orotidine-5'-phosphate decarboxylase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process ...UMP biosynthetic process / orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / pyrimidine nucleobase biosynthetic process / Pyrimidine biosynthesis / orotidine-5'-phosphate decarboxylase / UDP biosynthetic process / orotidine-5'-phosphate decarboxylase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / lactation / female pregnancy / cellular response to xenobiotic stimulus / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Orotate phosphoribosyl transferase domain / Orotate phosphoribosyltransferase / Purine/pyrimidine phosphoribosyl transferases signature. / Orotidine 5'-phosphate decarboxylase / Orotidine 5'-phosphate decarboxylase, active site / Orotidine 5'-phosphate decarboxylase active site. / Orotidine 5'-phosphate decarboxylase domain / Orotidine 5'-phosphate decarboxylase / HUMPS family / Orotidine 5'-phosphate decarboxylase / HUMPS family / Phosphoribosyl transferase domain ...Orotate phosphoribosyl transferase domain / Orotate phosphoribosyltransferase / Purine/pyrimidine phosphoribosyl transferases signature. / Orotidine 5'-phosphate decarboxylase / Orotidine 5'-phosphate decarboxylase, active site / Orotidine 5'-phosphate decarboxylase active site. / Orotidine 5'-phosphate decarboxylase domain / Orotidine 5'-phosphate decarboxylase / HUMPS family / Orotidine 5'-phosphate decarboxylase / HUMPS family / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
5-CYANO-URIDINE-5'-MONOPHOSPHATE / Uridine 5'-monophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsHeinrich, D. / Diederichsen, U. / Rudolph, M.
CitationJournal: Chemistry / Year: 2009
Title: Lys314 is a nucleophile in non-classical reactions of orotidine-5'-monophosphate decarboxylase
Authors: Heinrich, D. / Diederichsen, U. / Rudolph, M.G.
History
DepositionOct 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_validate_close_contact / software
Item: _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 ..._pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Orotidine-5'-phosphate decarboxylase
B: Orotidine-5'-phosphate decarboxylase
C: Orotidine-5'-phosphate decarboxylase
D: Orotidine-5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,78810
Polymers113,1994
Non-polymers1,5896
Water22,4831248
1
A: Orotidine-5'-phosphate decarboxylase
B: Orotidine-5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0927
Polymers56,5992
Non-polymers1,4935
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-22 kcal/mol
Surface area19820 Å2
MethodPISA
2
C: Orotidine-5'-phosphate decarboxylase
D: Orotidine-5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,6963
Polymers56,5992
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-21.4 kcal/mol
Surface area18960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.557, 60.793, 136.087
Angle α, β, γ (deg.)90.00, 99.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Orotidine-5'-phosphate decarboxylase / OMPdecase


Mass: 28299.742 Da / Num. of mol.: 4 / Fragment: UNP residues 224-480
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UMPS / Plasmid: pETM-30 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)
References: UniProt: P11172, orotidine-5'-phosphate decarboxylase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CNU / 5-CYANO-URIDINE-5'-MONOPHOSPHATE / 5-cyano-UMP / 5-cyanouridine 5'-(dihydrogen phosphate)


Type: RNA linking / Mass: 349.191 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H12N3O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1248 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.34 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris-HCl pH 8.0, 1.8 M (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 300.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→46.08 Å / Num. obs: 193472 / % possible obs: 85.3 % / Redundancy: 2.6 % / Rsym value: 0.069 / Net I/σ(I): 9.6
Reflection shellResolution: 1.4→1.46 Å / Redundancy: 0.7 % / Mean I/σ(I) obs: 1.5 / Num. unique all: 8026 / Rsym value: 0.378 / % possible all: 35.6

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Processing

Software
NameVersionClassification
COMOphasing
REFMAC5.4.0077refinement
XDSdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→46.08 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.427 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18701 9355 5 %RANDOM
Rwork0.1543 ---
obs0.15593 177695 82.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.678 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å2-0.76 Å2
2---0.38 Å20 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.4→46.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8275 0 102 1248 9625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0228579
X-RAY DIFFRACTIONr_bond_other_d0.0020.025862
X-RAY DIFFRACTIONr_angle_refined_deg1.4872.00711690
X-RAY DIFFRACTIONr_angle_other_deg2.721314406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.99251161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.32723.802363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.988151585
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3411565
X-RAY DIFFRACTIONr_chiral_restr0.0880.21342
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029602
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021699
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9741.55315
X-RAY DIFFRACTIONr_mcbond_other0.3821.52190
X-RAY DIFFRACTIONr_mcangle_it1.58928587
X-RAY DIFFRACTIONr_scbond_it2.4233264
X-RAY DIFFRACTIONr_scangle_it3.7534.53041
X-RAY DIFFRACTIONr_rigid_bond_restr1.136314441
X-RAY DIFFRACTIONr_sphericity_free4.38431248
X-RAY DIFFRACTIONr_sphericity_bonded1.851314239
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 211 -
Rwork0.274 4395 -
obs--27.65 %

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